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I am trying to make a PDF with layers. If one of my shapefiles symbology is set to categories, unique values, as in a states shapefile, it wont let me turn off each state; it groups it.

Is the only way to alleviate this to make individual shapefiles?

Its not just for the states, I have a bunch that are set to more than one unique values.

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There is no need to make individual shapefiles.

Instead create a layer from your original shapefile and place a definition query on it that filters its features for one state. Leave the symbology as single symbol.

Then for each other state, copy/paste the layer, change its definition query and change its symbol.

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